R Observatory: Metrics for bonsaiforest version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bonsaiforest

0.1.1Package record

Shrinkage Based Forest Plots

0packages depend

3Kdownloads / year

96.4%test coverage

10/13flavors OK

Overview

About

Maintained by Isaac GravestockCRAN page ↗GitHub ↗Issues ↗Declared funder: F. Hoffmann-La Roche AG

Subgroup analyses are routinely performed in clinical trial analyses. From a methodological perspective, two key issues of subgroup analyses are multiplicity (even if only predefined subgroups are investigated) and the low sample sizes of subgroups which lead to highly variable estimates, see e.g. Yusuf et al (1991) doi:10.1001/jama.1991.03470010097038. This package implements subgroup estimates based on Bayesian shrinkage priors, see Carvalho et al (2019) https://proceedings.mlr.press/v5/carvalho09a.html. In addition, estimates based on penalized likelihood inference are available, based on Simon et al (2011) doi:10.18637/jss.v039.i05. The corresponding shrinkage based forest plots address the aforementioned issues and can complement standard forest plots in practical clinical trial analyses.

Changes in 0.1.1

Adapt to changes in brms 2.22.0 for the specification of baseline hazards. (#79)

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("bonsaiforest", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("insightsengineering/bonsaiforest")

Development version from insightsengineering/bonsaiforest. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-bonsaiforest

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-bonsaiforest

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-bonsaiforest

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

3ERROR10OK

Check messages

ERRORtestsr-devel-windows-x86_64, r-oldrel-windows-x86_64, r-release-windows-x86_64

r-devel-windows-x86_64

Running 'testthat.R' [110s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(bonsaiforest)
  
  Attaching package: 'bonsaiforest'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > 
  > test_check("bonsaiforest")
  Compiling Stan program...
  specified C++17
  make cmd is
    make -f "D:/RCompile/recent/R/etc/x64/Makeconf" -f "D:/RCompile/recent/R/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file63d4691c71a3.d
...[truncated]...
s)
    8.         └─brms:::eval2(call, envir = args, enclos = envir)
    9.           └─base::eval(expr, envir, ...)
   10.             └─base::eval(expr, envir, ...)
   11.               └─brms (local) .fun(...)
   12.                 └─brms (local) .compile_model(model, ...)
   13.                   ├─brms:::eval_silent(...)
   14.                   │ └─base::eval(expr, envir)
   15.                   │   └─base::eval(expr, envir)
   16.                   └─brms::do_call(rstan::stan_model, args)
   17.                     └─brms:::eval2(call, envir = args, enclos = envir)
   18.                       └─base::eval(expr, envir, ...)
   19.                         └─base::eval(expr, envir, ...)
   20.                           └─rstan (local) .fun(model_code = .x1)
   21.                             └─rstan:::cxxfunctionplus(...)
   22.                               └─base::sink(type = "output")
  
  [ FAIL 2 | WARN 25 | SKIP 12 | PASS 68 ]
  Error:
  ! Test failures.
  Execution halted

r-oldrel-windows-x86_64

Running 'testthat.R' [137s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(bonsaiforest)
  
  Attaching package: 'bonsaiforest'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > 
  > test_check("bonsaiforest")
  Compiling Stan program...
  make cmd is
    make -f "D:/RCompile/recent/R-4.5.3/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.5.3/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file351b07790e0f.dll" WI
...[truncated]...
s)
    8.         └─brms:::eval2(call, envir = args, enclos = envir)
    9.           └─base::eval(expr, envir, ...)
   10.             └─base::eval(expr, envir, ...)
   11.               └─brms (local) .fun(...)
   12.                 └─brms (local) .compile_model(model, ...)
   13.                   ├─brms:::eval_silent(...)
   14.                   │ └─base::eval(expr, envir)
   15.                   │   └─base::eval(expr, envir)
   16.                   └─brms::do_call(rstan::stan_model, args)
   17.                     └─brms:::eval2(call, envir = args, enclos = envir)
   18.                       └─base::eval(expr, envir, ...)
   19.                         └─base::eval(expr, envir, ...)
   20.                           └─rstan (local) .fun(model_code = .x1)
   21.                             └─rstan:::cxxfunctionplus(...)
   22.                               └─base::sink(type = "output")
  
  [ FAIL 2 | WARN 25 | SKIP 12 | PASS 68 ]
  Error:
  ! Test failures.
  Execution halted

r-release-windows-x86_64

Running 'testthat.R' [104s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(bonsaiforest)
  
  Attaching package: 'bonsaiforest'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > 
  > test_check("bonsaiforest")
  Compiling Stan program...
  specified C++17
  make cmd is
    make -f "D:/RCompile/recent/R-4.6.1/etc/x64/Makeconf" -f "D:/RCompile/recent/R-4.6.1/share/make/winshlib.mk" CXX='$(CXX17) $(CXX17STD)' CXXFLAGS='$(CXX17FLAGS)' CXXPICFLAGS='$(CXX17PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX17LDFLAGS)' SHLIB_LD='$(SHLIB_CXX17LD)' SHLIB="file46
...[truncated]...
s)
    8.         └─brms:::eval2(call, envir = args, enclos = envir)
    9.           └─base::eval(expr, envir, ...)
   10.             └─base::eval(expr, envir, ...)
   11.               └─brms (local) .fun(...)
   12.                 └─brms (local) .compile_model(model, ...)
   13.                   ├─brms:::eval_silent(...)
   14.                   │ └─base::eval(expr, envir)
   15.                   │   └─base::eval(expr, envir)
   16.                   └─brms::do_call(rstan::stan_model, args)
   17.                     └─brms:::eval2(call, envir = args, enclos = envir)
   18.                       └─base::eval(expr, envir, ...)
   19.                         └─base::eval(expr, envir, ...)
   20.                           └─rstan (local) .fun(model_code = .x1)
   21.                             └─rstan:::cxxfunctionplus(...)
   22.                               └─base::sink(type = "output")
  
  [ FAIL 2 | WARN 25 | SKIP 12 | PASS 68 ]
  Error:
  ! Test failures.
  Execution halted

CRAN check page ↗

Slowest check: 14.1 min · r-release-linux-x86_64

Status changes

ERROR10 OK, 3 ERRORNow
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08

Show 4 earlier changesHide 4 earlier changes

OK11 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.1Citation fileNo

Description cites a JSS article

Help pages: 44 (3 internal)includes a package overview page
Examples that run: 96%27 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Introduction HTML

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #13,108 · ~8/day · ~248/mo

Releases R versions

Daily download trend is not available in this view yet.

34130 days

87790 days

3K1 year

Compare downloads with other packages →

Also on576 r2u27 autocran

How downloads are counted

Repository

insightsengineering/bonsaiforest ↗Organization: insightsengineering

3Stars

1Forks

2Open issues

2Open PRs

2Releases

85Commits

6Commit identities

statistical-engineering

85 commits · Last activity 2024-11-29 · Default branch at 0.1.1.9001, ahead of CRAN 0.1.1 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 93%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-07-21 · 32026-07-07 · 3

How these are measured

PracticesBeta

14 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/insightsengineering/bonsaiforest on 2026-10-21.

Continuous integration (1)

GitHub Actions

Governance and community (5)

Code of conduct (inherited from insightsengineering)Contributing guide (inherited from insightsengineering)Issue templatesCODEOWNERS

Funding links: pharmaverse.org

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2024-11-29

Coverage (1)

Coverage reporting

Show all practicesHide 3 practices

Reproducibility and dev environment (1)

data-raw/

Automation and maintenance (1)

pre-commit

Lint, format, editor (2)

lintrRStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing bonsaiforest adds 97 packages (49 with compiled code, 86 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1

Imports (17)

brms broom checkmate dplyr forcats gbm ggplot2 glmnetMASSRcpp splines2statssurvivaltibble tidyr tidyselect vdiffr

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (5)

Isaac Gravestock

Maintainer since 0.1.0 (2024)

Daniel Sabanés Bové

Author

Mar Vazquez Rabunal

Author

Marcel Wolbers

Author

F. Hoffmann-La Roche AG

Copyright holder, Funder

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.1.1Latest
record
2024-09-27 · current release · diff ↗
0.1.0
record
2024-06-17
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-06-17
Total releases: 2 / 2 yrs
License: Apache License 2.0 OSI
Minimum R: ≥ 4.1
Bundled data: 3.4 MB / 13 files
Download size: 3.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bonsaiforest")

Format

Gravestock, I., F. Hoffmann-La Roche AG, Sabanés Bové, D., Vazquez Rabunal, M., & Wolbers, M. (2024). bonsaiforest: Shrinkage Based Forest Plots (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.bonsaiforest

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for bonsaiforest version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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